Background

The human gastrointestinal tract is a complex ecosystem containing a delicate balance
of human and microbial cells involved in an intricate symbiotic relationship. In
general, the microbial constituency helps maintain a healthy environment and aids
in the efficient digestion. However, environmental and/or genetic factors may result
in an altered bacterial composition that manifests in a diseased condition, such as
Crohn’s disease. The recent availability of genomic-based molecular technologies
such as whole community genome sequencing and whole community proteomics have provided
unique capabilities of profiling the compositions and activities of this microbiome without having to cultivate its membership.

Materials and methods

We are utilizing a non-targeted, mass spectrometry-based proteomics approach to identify
the microbial proteins in fecal samples from human twins. Proteome samples were analyzed
with technical duplicates via a multidimensional LC tandem mass spectrometric approach
on a hybrid linear ion trap-Orbitrap. The proteome measurements identified > 2000
proteins for each sample and replicate.

Results and conclusion

Amongst the microbial genomes, Bacteroides thetaiotaomicron,Bifidobacterium longum, Bacteroides fragilis and Bifidobacterium adolescentis were the most highly identified species, as expected since these are known to be
among the most abundant bacteria in the human gut. Interestingly, the majority of
the microbial proteins that were identified were classified into COG categories for
translation, energy generation, and carbohydrate metabolism. The latter category
is especially interesting in that it reveals one of the synergistic relationships
between humans and microbes in this ecosystem. Surprisingly, a number of innate human
immunity proteins were also observed, suggesting a level of human regulation of microbial
abundance. A number of abundant unknown proteins were also identified. The results
of this study demonstrate that it is possible to obtain high quality, extensive protein
identifications from translated metagenome sequence data collected from distinct human
individuals.

Acknowledgements

Research support provided by NIH-HMP Demonstration Program. Oak Ridge National Laboratory
is managed by UT-Battelle, LLC, for the U.S. Department of Energy under Contract No.
DE-AC05-00OR22725.